A Parallel Universe was a separate reality of the main BIONICLE Universe, with minor and major differences.
Known Universes
"Toa Empire" Parallel Universe
In this parallel universe, Toa Tuyet, using the Nui Stone, allied with Toa Nidhiki to kill Toa Lhikan. Tuyet proceeded to blame the deaths of Matoran she killed to appear like a countdown on the Dark Hunters and organize Toa across the Matoran Universe into the Toa Empire with herself as Empress. Corrupting her Empire, she eliminated organizations she believed posed a threat to Mata Nui, primarily the Brotherhood of Makuta.
"The Kingdom" Parallel Universe
In this Parallel Universe Matoro hesitated for one second too long and failed to save Mata Nui, thus, all of the speicies in the universe had to work together to get to the island of Mata Nui and survive.
"The Melding" Parallel Universe
In this Parallel Universe the Shattering on Spherus Magna was prevented by an event called The Melding, and Mata Nui was never created.
"The Great Mirror" Parallel Univers
In this Parallel Universe Mata Nui is killed by Tuma after Mata Nui crashes on Bara Magna and aids the Glatorian of theSkrall. Mata Nui was later brought back to life by a young Glatorian named Knesh and his friend Kieana who defeated many Skrall before reviving him.